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1.  The emergence and evolution of the novel epidemic norovirus GII.4 variant Sydney 2012 
Virology  2013;0:106-113.
Norovirus is the leading cause of acute gastroenteritis with most infections caused by GII.4 variants. To understand the evolutionary processes that contribute to the emergence of GII.4 variants, we examined the molecular epidemiology of norovirus-associated acute gastroenteritis in Australia and New Zealand from 893 outbreaks between 2009 and 2012. Throughout the study GII.4 New Orleans 2009 was predominant; however, during 2012 it was replaced by an emergent GII.4 variant, Sydney 2012. An evolutionary analysis of capsid gene sequences was performed to determine the origins and selective pressures driving the emergence of these recently circulating GII.4 variants. This revealed that both New Orleans 2009 and Sydney 2012 share a common ancestor with GII.4 Apeldoorn 2007. Furthermore, pre-epidemic ancestral variants of each virus were identified up to two years before their pandemic emergence. Adaptive changes at known blockade epitopes in the viral capsid were also identified that likely contributed to their emergence.
doi:10.1016/j.virol.2013.12.005
PMCID: PMC3984403  PMID: 24503072
Norovirus; Gastroenteritis; Emergence; Evolution; Sydney 2012
2.  The statistical analysis of partially confounded covariates important to neural spiking 
Journal of neuroscience methods  2012;205(2):295-304.
A method is presented capable of disambiguating the relative influence of statistical covariates upon neural spiking activity. The method, an extension of the generalized linear model (GLM) methodology introduced in Truccolo et al. (2005) to analyze neural spiking data, exploits projection operations motivated by a geometry present in the Fisher information of the GLM maximum likelihood parameter estimator. By exploiting these projections, neural activity can be divided into three categories. These three categories, neural activity due solely to a set of covariates of interest, neural activity due solely to a set of uninteresting, or nuisance, covariates, and neural activity that cannot be unequivocally assigned to either set of covariates, can be associated with physical variables such as time, position, head-direction and velocity. This association allows the analysis of neural activity that can, for example, be due solely to temporal influence, irrespective of other, identified, influences. The method is applied in simulation to a rat exploring a temporally modulated place field. A portion of the analysis reported in MacDonald et al. (2011), using the methodology described herein, is reproduced. This analysis demonstrates the temporal bridging of a delay period in a sequential memory task by firing activity of cells present in the rodent hippocampus that cannot be explained by rodent position, head direction or velocity.
doi:10.1016/j.jneumeth.2011.12.021
PMCID: PMC3976545  PMID: 22281297
Neural activity disambiguation; Confound; Covariate disambiguation; Generalized linear model; Projection; Point process
3.  Association of Single-Nucleotide Polymorphisms of the Tau Gene With Late-Onset Parkinson Disease 
Context
The human tau gene, which promotes assembly of neuronal microtubules, has been associated with several rare neurologic diseases that clinically include parkinsonian features. We recently observed linkage in idiopathic Parkinson disease (PD) to a region on chromosome 17q21 that contains the tau gene. These factors make tau a good candidate for investigation as a susceptibility gene for idiopathic PD, the most common form of the disease.
Objective
To investigate whether the tau gene is involved in idiopathic PD.
Design, Setting, and Participants
Among a sample of 1056 individuals from 235 families selected from 13 clinical centers in the United States and Australia and from a family ascertainment core center, we tested 5 single-nucleotide polymorphisms (SNPs) within the tau gene for association with PD, using family-based tests of association. Both affected (n = 426) and unaffected (n = 579) family members were included; 51 individuals had unclear PD status. Analyses were conducted to test individual SNPs and SNP haplotypes within the tau gene.
Main Outcome Measure
Family-based tests of association, calculated using asymptotic distributions.
Results
Analysis of association between the SNPs and PD yielded significant evidence of association for 3 of the 5 SNPs tested: SNP 3, P = .03; SNP 9i, P = .04; and SNP 11, P = .04. The 2 other SNPs did not show evidence of significant association (SNP 9ii, P = .11, and SNP 9iii, P = .87). Strong evidence of association was found with haplotype analysis, with a positive association with one haplotype (P = .009) and a negative association with another haplotype (P = .007). Substantial linkage disequilibrium (P<.001) was detected between 4 of the 5 SNPs (SNPs 3,9i, 9ii, and 11).
Conclusions
This integrated approach of genetic linkage and positional association analyses implicates tau as a susceptibility gene for idiopathic PD.
PMCID: PMC3973175  PMID: 11710889
4.  Knowledge of Obesity and Its Impact on Reproductive Health Outcomes Among Urban Women 
Journal of community health  2013;38(2):261-267.
This prospective survey study assessed the knowledge of reproductive outcomes that are affected by obesity among women in an urban community. A total of 207 women attending a community fair on the south side of Chicago participated in the study. A survey assessing knowledge of BMI and of the effects of obesity on general, cardiometabolic and reproductive health outcomes was administered. Subjects ranged in age from 18 to 70 years (mean ± SD, 48.6 ± 12.9 years) and ranged in BMI from 17.3 to 52.1 kg/m2 (mean ± SD, 31.2 ± 6.7 kg/m2). The following percentages of women were aware that obesity increases the risk of miscarriage (37.5%), irregular periods (35.8%), infertility (33.9%), cesarean section (30.8%), breast cancer (28.0%), birth defects (23.7%), stillbirth (14.1%), and endometrial cancer (18.1%). This study found that while women in an urban community are aware of the cardiometabolic risks associated with obesity, they demonstrate limited knowledge of the effects of obesity on reproductive outcomes. Public education is needed to increase knowledge and awareness of the reproductive consequences of obesity. Women of reproductive age may be uniquely responsive to obesity education and weight loss intervention.
doi:10.1007/s10900-012-9609-1
PMCID: PMC3563852  PMID: 22961295
community health; knowledge; obesity; reproduction; women
5.  Distinct injury markers for the early detection and prognosis of incident acute kidney injury in critically ill adults with preserved kidney function 
Kidney international  2013;84(4):786-794.
The use of novel biomarkers to detect incident acute kidney injury (AKI) in the critically ill is hindered by heterogeneity of injury and the potentially confounding effects of prevalent AKI. Here we examined the ability of urine NGAL (NGAL), L-type Fatty Acid Binding Protein (L-FABP), and Cystatin C to predict AKI development, death, and dialysis in a nested case-control study of 380 critically ill adults with an eGFR over 60 ml/min/1.73 m2. One-hundred thirty AKI cases were identified following biomarker measurement and were compared to 250 controls without AKI. Areas under the receiver-operator characteristic curves (AUC-ROCs) for discriminating incident AKI from non-AKI were 0.58(95%CI: 0.52-0.64), 0.59(0.52-0.65), and 0.50(0.48-0.57) for urine NGAL, L-FABP, and Cystatin C, respectively. The combined AUC-ROC for NGAL and L-FABP was 0.59(56-0.69). Both urine NGAL and L-FABP independently predicted AKI during multivariate regression; however, risk reclassification indices were mixed. Neither urine biomarker was independently associated with death or acute dialysis [NGAL hazard ratio 1.35(95%CI: 0.93-1.96), L-FABP 1.15(0.82-1.61)] though both independently predicted the need for acute dialysis [NGAL 3.44(1.73-6.83), L-FABP 2.36(1.30-4.25)]. Thus, urine NGAL and L-FABP independently associated with the development of incident AKI and receipt of dialysis but exhibited poor discrimination for incident AKI using conventional definitions.
doi:10.1038/ki.2013.174
PMCID: PMC3788840  PMID: 23698227
6.  Exome Sequencing and Genome-Wide Linkage Analysis in 17 Families Illustrates the Complex Contribution of TTN Truncating Variants to Dilated Cardiomyopathy 
Circulation. Cardiovascular genetics  2013;6(2):10.1161/CIRCGENETICS.111.000062.
Background
Familial dilated cardiomyopathy is a genetically heterogeneous disease with >30 known genes. TTN truncating variants were recently implicated in a candidate gene study to cause 25% of familial and 18% of sporadic dilated cardiomyopathy (DCM) cases.
Methods and Results
We used an unbiased genome-wide approach employing both linkage analysis and variant filtering across the exome sequences of 48 individuals affected with DCM from 17 families to identify genetic cause. Linkage analysis ranked the TTN region as falling under the second highest genome-wide multipoint linkage peak, MLOD 1.59. We identified six TTN truncating variants carried by affected with DCM in 7 of 17 DCM families (LOD 2.99); 2 of these 7 families also had novel missense variants segregated with disease. Two additional novel truncating TTN variants did not segregate with DCM. Nucleotide diversity at the TTN locus, including missense variants, was comparable to five other known DCM genes. The average number of missense variants in the exome sequences from the DCM cases or the ~5,400 cases from the Exome Sequencing Project was ~23 per individual. The average number of TTN truncating variants in the Exome Sequencing Project was 0.014 per individual. We also identified a region (chr9q21.11-q22.31) with no known DCM genes with a maximum heterogeneity LOD score of 1.74.
Conclusions
These data suggest that TTN truncating variants contribute to DCM cause. However, the lack of segregation of all identified TTN truncating variants illustrates the challenge of determining variant pathogenicity even with full exome sequencing.
doi:10.1161/CIRCGENETICS.111.000062
PMCID: PMC3815606  PMID: 23418287
genetics; human; genome-wide analysis; dilated cardiomyopathy; exome
7.  Systematic review and meta-analysis of opioid antagonists for smoking cessation 
BMJ Open  2014;4(3):e004393.
Objectives
This meta-analysis sought to evaluate the efficacy of opioid antagonists in promoting long-term smoking cessation. Post-treatment abstinence was examined as a secondary outcome and effects on withdrawal symptoms, craving and reduced consumption were also explored.
Design
The search strategy for this meta-analysis included clinical trials (published and unpublished data) in the Cochrane Tobacco Addiction Group Specialized Register and MEDLINE.
Participants
Adult smokers.
Interventions
We included randomised trials comparing opioid antagonists to placebo or an alternative therapy for smoking cessation and reported data on abstinence for a minimum of 6 months.
Primary and secondary outcome measures
Outcomes included smoking abstinence at long-term follow-up (primary); abstinence at end of treatment (secondary); and effects on withdrawal, craving and smoking consumption (exploratory).
Results
8 trials with a total of 1213 participants were included. Half the trials examined the benefit of adding naltrexone versus placebo to nicotine replacement therapy (NRT). There was no significant difference between naltrexone and placebo alone (relative risk (RR) 1.00; 95% CI 0.66 to 1.51) or as an adjunct to NRT (RR 0.95; 95% CI 0.70 to 1.30), with an overall pooled estimate of RR 0.97; 95% CI 0.76 to 1.24. Findings for naltrexone effects on withdrawal, craving and reduced smoking were equivocal.
Conclusions
The findings indicate no beneficial effect of naltrexone alone or as an adjunct to NRT on short-term or long-term smoking abstinence. While further trials may narrow the confidence limits, they are unlikely to appreciably alter the conclusion.
doi:10.1136/bmjopen-2013-004393
PMCID: PMC3963070  PMID: 24633528
opioid antagonists ; smoking cessation; tobacco; smoking abstinence; naltrexone
8.  Whole exome sequencing of rare variants in EIF4G1 and VPS35 in Parkinson disease 
Neurology  2013;80(11):982-989.
Objective:
Recently, vacuolar protein sorting 35 (VPS35) and eukaryotic translation initiation factor 4 gamma 1 (EIF4G1) have been identified as 2 causal Parkinson disease (PD) genes. We used whole exome sequencing for rapid, parallel analysis of variations in these 2 genes.
Methods:
We performed whole exome sequencing in 213 patients with PD and 272 control individuals. Those rare variants (RVs) with <5% frequency in the exome variant server database and our own control data were considered for analysis. We performed joint gene-based tests for association using RVASSOC and SKAT (Sequence Kernel Association Test) as well as single-variant test statistics.
Results:
We identified 3 novel VPS35 variations that changed the coded amino acid (nonsynonymous) in 3 cases. Two variations were in multiplex families and neither segregated with PD. In EIF4G1, we identified 11 (9 nonsynonymous and 2 small indels) RVs including the reported pathogenic mutation p.R1205H, which segregated in all affected members of a large family, but also in 1 unaffected 86-year-old family member. Two additional RVs were found in isolated patients only. Whereas initial association studies suggested an association (p = 0.04) with all RVs in EIF4G1, subsequent testing in a second dataset for the driving variant (p.F1461) suggested no association between RVs in the gene and PD.
Conclusions:
We confirm that the specific EIF4G1 variation p.R1205H seems to be a strong PD risk factor, but is nonpenetrant in at least one 86-year-old. A few other select RVs in both genes could not be ruled out as causal. However, there was no evidence for an overall contribution of genetic variability in VPS35 or EIF4G1 to PD development in our dataset.
doi:10.1212/WNL.0b013e31828727d4
PMCID: PMC3653206  PMID: 23408866
9.  Noise Genetics: Inferring Protein Function by Correlating Phenotype with Protein Levels and Localization in Individual Human Cells 
PLoS Genetics  2014;10(3):e1004176.
To understand gene function, genetic analysis uses large perturbations such as gene deletion, knockdown or over-expression. Large perturbations have drawbacks: they move the cell far from its normal working point, and can thus be masked by off-target effects or compensation by other genes. Here, we offer a complementary approach, called noise genetics. We use natural cell-cell variations in protein level and localization, and correlate them to the natural variations of the phenotype of the same cells. Observing these variations is made possible by recent advances in dynamic proteomics that allow measuring proteins over time in individual living cells. Using motility of human cancer cells as a model system, and time-lapse microscopy on 566 fluorescently tagged proteins, we found 74 candidate motility genes whose level or localization strongly correlate with motility in individual cells. We recovered 30 known motility genes, and validated several novel ones by mild knockdown experiments. Noise genetics can complement standard genetics for a variety of phenotypes.
Author Summary
Inferring the function of proteins and the role they play in cellular processes is essential for our understanding of cell biology, genetics and biology in general. Standard genetic approaches use large perturbations to cells such as gene knockout, knockdown or over expression of genes. Such methods are powerful, but have the drawback of taking the cell far from its normal working point. Here, we provide a new and much milder approach, which uses the natural cell-cell variation in protein level and expression pattern as a source of mild perturbation. We monitor individual live cancer cells under the microscope and correlate their protein levels and localization with phenotype in the same cells. We use the motility of human cancer cells as a model system that is highly important for understanding metastasis in cancer. We find that our approach uncovers most of the known motility proteins, as well as new ones which we validate using knockdown experiments. Our novel approach is widely applicable to any phenotype that can be visualized in individual cells, and for any organism for which one can measure proteins in individual cells.
doi:10.1371/journal.pgen.1004176
PMCID: PMC3945223  PMID: 24603725
10.  Characterization of Host-Cell Line Specific Glycosylation Profiles of Early Transmitted/Founder HIV-1 gp120 Envelope Proteins 
Journal of proteome research  2013;12(3):1223-1234.
Glycosylation plays an essential role in regulating protein function by modulating biological, structural, and therapeutic properties. However, due to its inherent heterogeneity and diversity, the comprehensive analysis of protein glycosylation remains a challenge. As part of our continuing effort in the analysis of glycosylation profiles of recombinant HIV-1 envelope-based immunogens, we evaluated and compared the host-cell specific glycosylation pattern of recombinant HIV-1 surface glycoprotein, gp120, derived from clade C transmitted/founder virus 1086.C expressed in Chinese hamster ovary (CHO) and human embryonic kidney containing T antigen (293T) cell lines. We used an integrated glycopeptide-based mass mapping workflow that includes a partial deglycosylation step described in our previous study1 with the inclusion of the fragmentation technique, electron transfer dissociation (ETD), to complement collision induced dissociation (CID). The inclusion of ETD facilitated the analysis by providing additional validation for glycopeptide identification and expanding the identified glycopeptides to include coverage of O-linked glycosylation. The site-specific glycosylation analysis shows that the transmitted/founder 1086.C gp120 expressed in CHO and 293T displayed distinct similarities and differences. For N-linked glycosylation, two sites (N386 and N392), in the V4 region were populated with high mannose glycans in the CHO cell-derived 1086.C gp120, while these sites had a mixture of high mannose and processed glycans in the 293T cell-derived 1086.C gp120. Compositional analysis of O-linked glycans revealed that 293T cell-derived 1086.C gp120 consisted of cores 1, 2, and 4 type O-linked glycans while CHO cell-derived 1086.C exclusively consisted of core 1 type O-linked glycans. Overall, glycosylation site occupancy of the CHO and 293T cell-derived 1086.C gp120 show high degree of similarity except for one site at N88 in the C1 region. This site was partially occupied in 293T-gp120 but fully occupied in CHO-gp120. Site-specific glycopeptide analysis of transmitted/founder 1086.C gp120 expressed in CHO cells revealed the presence of phosphorylated glycans while 293T cell produced 1086.C gp120 glycans were not phosphorylated. While the influence of phosphorylated glycans on immunogenicity is unclear, distinguishing host-cell specific variations in glycosylation profiles provides insights into the similarity (or difference) in recombinant vaccine products. While these differences had minimal effect on envelope antigenicity, they may be important in considering immunogenicity and functional capacities of recombinant envelope proteins produced in different expression systems.
doi:10.1021/pr300870t
PMCID: PMC3674872  PMID: 23339644
11.  Heat shock protein expression analysis in canine osteosarcoma reveals HSP60 as a potentially relevant therapeutic target 
Cell Stress & Chaperones  2013;18(5):607-622.
Heat shock proteins (HSP) are highly conserved across eukaryotic and prokaryotic species. These proteins play a role in response to cellular stressors, protecting cells from damage and facilitating recovery. In tumor cells, HSPs can have cytoprotective effects and interfere with apoptotic cascades. This study was performed to assess the prognostic and predictive values of the gene expression of HSP family members in canine osteosarcoma (OS) and their potential for targeted therapy. Gene expressions for HSP were assessed using quantitative PCR (qPCR) on 58 snap-frozen primary canine OS tumors and related to clinic-pathological parameters. A significant increased expression of HSP60 was found in relation to shorter overall survival and an osteoblastic phenotype. Therefore, the function of HSP60 was investigated in more detail. Immunohistochemical analysis revealed heterogeneous staining for HSP60 in tumors. The highest immunoreactivity was found in tumors of short surviving dogs. Next HSP expression was shown in a variety of canine and human OS cell lines by qPCR and Western blot. In two highly metastatic cell lines HSP60 expression was silenced using siRNA resulting in decreased cell proliferation and induction of apoptosis in both cell lines. It is concluded that overexpression of HSP60 is associated with a poor prognosis of OS and should be evaluated as a new target for therapy.
doi:10.1007/s12192-013-0414-2
PMCID: PMC3745254  PMID: 23463150
Heat shock proteins (HSP); Osteosarcoma; Dog
12.  Infertility patients’ knowledge of the effects of obesity on reproductive health outcomes 
American journal of obstetrics and gynecology  2012;207(6):509.e1-509.e10.
OBJECTIVE
The objective of the study was to assess the infertility patient knowledge of reproductive outcomes affected by obesity.
STUDY DESIGN
This was a prospective survey study of 150 female infertility patients in an academic medical center. Subjects were administered the Rapid Estimate of Adult Literacy in Medicine–Short Form and a questionnaire on the health risks of obesity, and investigators obtained height and weight measurements.
RESULTS
Subjects’ age ranged from 21 to 45 years (mean 34.8 ± 4.94 SD) and body mass index ranged from 17.9 to 62.9 kg/m2 (mean 26.5 ± 7.54 SD). The following percentages of women were aware that obesity increases the risk of infertility (82.7%), irregular periods (70.0%), miscarriage (60.7%), cesarean section (48.7%), breast cancer (38.7%), birth defects (29.3%), stillbirth (22.7%), and endometrial cancer (20.7%).
CONCLUSION
Among women with infertility, there is limited knowledge of reproductive outcomes affected by obesity. Public education is needed to increase awareness. Women undergoing fertility treatment are motivated for reproductive success and may be uniquely receptive to obesity education and weight loss intervention.
doi:10.1016/j.ajog.2012.08.020
PMCID: PMC3935017  PMID: 22981319
body mass index; health literacy; infertility; obesity; reproductive outcomes
13.  An Open Trial of Relapse Prevention Therapy for Smokers With Schizophrenia 
Journal of dual diagnosis  2013;9(1):87-93.
Objective
Following successful smoking cessation, smokers with schizophrenia are vulnerable to relapse shortly after treatment discontinuation. Our objective was to assess the feasibility and effectiveness of a 12-month relapse prevention intervention in recently abstinent smokers with schizophrenia.
Method
Adult outpatient smokers with schizophrenia received weekly cognitive behavioral therapy groups, bupropion slow release, transdermal nicotine patch, and nicotine gum or lozenge for three months. Subjects with seven-day point prevalence abstinence at month 3 received an additional 12 months (months 4-15) of therapy with bupropion, transdermal nicotine patch, and nicotine gum/lozenge in conjunction with relapse prevention-based cognitive behavioral therapy groups that were held weekly in month 4, biweekly in months 5-6, and monthly in months 7-15.
Results
Seventeen of 41 participants (41.5%) attained biochemically verified self-report of seven-day point prevalence abstinence at the end of three months of treatment and entered relapse prevention treatment. There was an 81% attendance rate at relapse prevention groups. At the end of the 12-month relapse prevention phase (month 15 overall), 11 of 17 (64.7%) demonstrated biochemically verified seven-day point prevalence abstinence, and 10 of 17 (58.8%) reported four-week continuous abstinence. Almost one quarter of the sample (23.5%) demonstrated long-term prolonged abstinence through the end of the trial. There were no clinically detected cases of psychiatric symptom exacerbation. One participant, who was managed as an outpatient, self-reported psychiatric symptom exacerbation in the interim period between study visits.
Conclusions
Extended duration smoking cessation treatment is well-tolerated and may improve smoking outcomes for recently abstinent smokers with schizophrenia. Controlled trials are warranted.
doi:10.1080/15504263.2012.749559
PMCID: PMC3671354  PMID: 23750123
schizophrenia; severe mental illness; smoking cessation; nicotine replacement therapy; bupropion; cognitive behavioral therapy; relapse prevention
14.  A procedure for testing across-condition rhythmic spike-field association change 
Journal of neuroscience methods  2012;213(1):43-62.
Many experiments in neuroscience have compared the strength of association between neural spike trains and rhythms present in local field potential (LFP) recordings. The measure employed in these comparisons, “spike-field coherence”, is a frequency dependent measure of linear association, and is shown to depend on overall neural activity (Lepage et al., 2011). Dependence upon overall neural activity, that is, dependence upon the total number of spikes, renders comparison of spike-field coherence across experimental context difficult. In this paper, an inferential procedure based upon a generalized linear model is shown to be capable of separating the effects of overall neural activity from spike train-LFP oscillatory coupling. This separation provides a means to compare the strength of oscillatory association between spike train-LFP pairs independent of differences in spike counts.
Following a review of the generalized linear modelling framework of point process neural activity a specific class of generalized linear models are introduced. This model class, using either a piece-wise constant link function, or an exponential function to relate an LFP rhythm to neural response, is used to develop hypothesis tests capable of detecting changes in spike train-LFP oscillatory coupling. The performance of these tests is validated, both in simulation and on real data. The proposed method of inference provides a principled statistical procedure by which across-context change in spike train-LFP rhythmic association can be directly inferred that explicitly handles between-condition differences in total spike count.
doi:10.1016/j.jneumeth.2012.10.010
PMCID: PMC3800189  PMID: 23164959
Oscillations; Rhythms; Local field potential; Spikes; Statistical association; Hypothesis testing; coherence; Spike-field coherence; Generalized linear model; Point process
15.  Activated Peritoneal Cavity B-1a Cells Possess Regulatory B Cell Properties 
PLoS ONE  2014;9(2):e88869.
Previous studies have suggested that murine peritoneal cavity-derived B-1a cells possess similarities with described regulatory B cell subsets. The aim of the current study was to examine the potential immunoregulatory function of peritoneal cavity-derived B(-1a) cells. In vitro activation of peritoneal cavity-derived B- and B-1a cells shows that activation of these B cells with anti-CD40 and LPS induces these cells to secrete more IL-10, IL-6 and IgM as compared to splenic B cells. In a suppression assay, CD40/TLR4-activated peritoneal cavity B cells possess regulatory B cell functions as they inhibit the capacity of CD4+ T cells to produce both tumor necrosis factor-α and interferon-γ. Splenic B cells did not show this, whereas non-activated peritoneal cavity B cells augmented the capacity of CD4+ T cells to produce tumor necrosis factor-α, while the ability to produce interferon-γ was not altered. The current paper compares splenic B cells to peritoneal cavity B(-1a) cells in an in vitro activation- and an suppression-assay and concludes that peritoneal cavity B(-1a) cells possess properties that appear similar to splenic autoimmune-suppressive regulatory B cell subsets described in the literature.
doi:10.1371/journal.pone.0088869
PMCID: PMC3923827  PMID: 24551182
16.  Alterations of Pancreatic Islet Structure, Metabolism and Gene Expression in Diet-Induced Obese C57BL/6J Mice 
PLoS ONE  2014;9(2):e86815.
The reduction of functional β cell mass is a key feature of type 2 diabetes. Here, we studied metabolic functions and islet gene expression profiles of C57BL/6J mice with naturally occurring nicotinamide nucleotide transhydrogenase (NNT) deletion mutation, a widely used model of diet-induced obesity and diabetes. On high fat diet (HF), the mice developed obesity and hyperinsulinemia, while blood glucose levels were only mildly elevated indicating a substantial capacity to compensate for insulin resistance. The basal serum insulin levels were elevated in HF mice, but insulin secretion in response to glucose load was significantly blunted. Hyperinsulinemia in HF fed mice was associated with an increase in islet mass and size along with higher BrdU incorporation to β cells. The temporal profiles of glucose-stimulated insulin secretion (GSIS) of isolated islets were comparable in HF and normal chow fed mice. Islets isolated from HF fed mice had elevated basal oxygen consumption per islet but failed to increase oxygen consumption further in response to glucose or carbonyl cyanide-4-trifluoromethoxyphenylhydrazone (FCCP). To obtain an unbiased assessment of metabolic pathways in islets, we performed microarray analysis comparing gene expression in islets from HF to normal chow-fed mice. A few genes, for example, those genes involved in the protection against oxidative stress (hypoxia upregulated protein 1) and Pgc1α were up-regulated in HF islets. In contrast, several genes in extracellular matrix and other pathways were suppressed in HF islets. These results indicate that islets from C57BL/6J mice with NNT deletion mutation develop structural, metabolic and gene expression features consistent with compensation and decompensation in response to HF diet.
doi:10.1371/journal.pone.0086815
PMCID: PMC3914796  PMID: 24505268
17.  Presynaptic Alpha-Synuclein Aggregation in a Mouse Model of Parkinson's Disease 
The Journal of Neuroscience  2014;34(6):2037-2050.
Parkinson's disease and dementia with Lewy bodies are associated with abnormal neuronal aggregation of α-synuclein. However, the mechanisms of aggregation and their relationship to disease are poorly understood. We developed an in vivo multiphoton imaging paradigm to study α-synuclein aggregation in mouse cortex with subcellular resolution. We used a green fluorescent protein-tagged human α-synuclein mouse line that has moderate overexpression levels mimicking human disease. Fluorescence recovery after photobleaching (FRAP) of labeled protein demonstrated that somatic α-synuclein existed primarily in an unbound, soluble pool. In contrast, α-synuclein in presynaptic terminals was in at least three different pools: (1) as unbound, soluble protein; (2) bound to presynaptic vesicles; and (3) as microaggregates. Serial imaging of microaggregates over 1 week demonstrated a heterogeneous population with differing α-synuclein exchange rates. The microaggregate species were resistant to proteinase K, phosphorylated at serine-129, oxidized, and associated with a decrease in the presynaptic vesicle protein synapsin and glutamate immunogold labeling. Multiphoton FRAP provided the specific binding constants for α-synuclein's binding to synaptic vesicles and its effective diffusion coefficient in the soma and axon, setting the stage for future studies targeting synuclein modifications and their effects. Our in vivo results suggest that, under moderate overexpression conditions, α-synuclein aggregates are selectively found in presynaptic terminals.
doi:10.1523/JNEUROSCI.2581-13.2014
PMCID: PMC3913861  PMID: 24501346
18.  SAMe Treatment Prevents the Ethanol-Induced Epigenetic Alterations of Genes in the Toll-Like Receptor Pathway 
Prior studies showed that Toll-like receptor (TLR) signaling pathway genes were up regulated in the liver of rats fed ethanol, but not in rats fed ethanol plus S-adenosylmethionine (SAMe). These results were obtained using a PCR microplate array analysis for TLRs and associated proteins such as proinflammatory cytokines and chemokine mRNA levels. A large number of genes were up regulated by the ethanol diet, but not the ethanol plus SAMe diet. In the present study, using the same experimental rat livers, DNA methylation analysis was done by using an Epitect Methyl DNA Restriction Kit (Qiagen, 335451) (24 genes). The results of all the genes combined shows a highly significant increase in methylation in the ethanol-fed group of rats, but not in the dextrose-fed, SAMe-fed or ethanol plus SAMe-fed groups of rats. There was also an increase in DNA methylation in rats with high blood alcohol levels compared to a rat with a low blood alcohol level. The individual genes that were up regulated as indicated by the increased mRNA measured by qPCR correlated positively with the increased methylation of the DNA of the corresponding gene as follows: Cd14, Hspa1a, Irf1, Irak1, Irak2, Map3k7, Myd88, Pparα, Ripk2, Tollip and Traf6.
doi:10.1016/j.yexmp.2012.09.024
PMCID: PMC3562371  PMID: 23047067
TLR (Toll-like receptor); SAMe (S-adenosyl methionine); BAL/blood alcohol levels; 5-methylcytosine
19.  A Unified Approach to Linking Experimental, Statistical and Computational Analysis of Spike Train Data 
PLoS ONE  2014;9(1):e85269.
A fundamental issue in neuroscience is how to identify the multiple biophysical mechanisms through which neurons generate observed patterns of spiking activity. In previous work, we proposed a method for linking observed patterns of spiking activity to specific biophysical mechanisms based on a state space modeling framework and a sequential Monte Carlo, or particle filter, estimation algorithm. We have shown, in simulation, that this approach is able to identify a space of simple biophysical models that were consistent with observed spiking data (and included the model that generated the data), but have yet to demonstrate the application of the method to identify realistic currents from real spike train data. Here, we apply the particle filter to spiking data recorded from rat layer V cortical neurons, and correctly identify the dynamics of an slow, intrinsic current. The underlying intrinsic current is successfully identified in four distinct neurons, even though the cells exhibit two distinct classes of spiking activity: regular spiking and bursting. This approach – linking statistical, computational, and experimental neuroscience – provides an effective technique to constrain detailed biophysical models to specific mechanisms consistent with observed spike train data.
doi:10.1371/journal.pone.0085269
PMCID: PMC3894976  PMID: 24465520
20.  A Simple Approach to Assign Disulfide Connectivity Using Extracted Ion Chromatograms of Electron Transfer Dissociation Spectra 
Analytical chemistry  2013;85(2):1192-1199.
Increasing interest in production of protein-based pharmaceuticals (biotherapeutics) is accompanied by an increased need for verification of protein folding and correct disulfide bonding. Recombinant protein expression may produce aberrant disulfide bonds and could result in safety concerns or decreased efficacy. Thus, the thorough analysis of disulfide bonding is a necessity for protein therapeutics. The use of ETD facilitates this analysis because disulfide bonds are preferentially cleaved when subjected to ETD. Here, we make use of this well-characterized reaction to assign disulfide bonding networks by coupling the use of extracted ion chromatograms (XICs) of cysteine-containing peptides with ETD analysis to produce an efficient assignment approach for disulfide bonding. This method can be used to assign a disulfide pattern in a de novo fashion, to detect disulfide shuffling, and to provide information on heterogeneity, when more than one disulfide bonding pattern is present. The method was applied for assigning the disulfide-bonding network of a recombinant monomer of the HIV envelope protein gp120. It was found that one region of the protein, the V1/V2 loops, had significant heterogeneity in the disulfide bonds.
doi:10.1021/ac303124w
PMCID: PMC3607449  PMID: 23210856
21.  Exome sequencing of extended families with autism reveals genes shared across neurodevelopmental and neuropsychiatric disorders 
Molecular Autism  2014;5:1.
Background
Autism spectrum disorders (ASDs) comprise a range of neurodevelopmental conditions of varying severity, characterized by marked qualitative difficulties in social relatedness, communication, and behavior. Despite overwhelming evidence of high heritability, results from genetic studies to date show that ASD etiology is extremely heterogeneous and only a fraction of autism genes have been discovered.
Methods
To help unravel this genetic complexity, we performed whole exome sequencing on 100 ASD individuals from 40 families with multiple distantly related affected individuals. All families contained a minimum of one pair of ASD cousins. Each individual was captured with the Agilent SureSelect Human All Exon kit, sequenced on the Illumina Hiseq 2000, and the resulting data processed and annotated with Burrows-Wheeler Aligner (BWA), Genome Analysis Toolkit (GATK), and SeattleSeq. Genotyping information on each family was utilized in order to determine genomic regions that were identical by descent (IBD). Variants identified by exome sequencing which occurred in IBD regions and present in all affected individuals within each family were then evaluated to determine which may potentially be disease related. Nucleotide alterations that were novel and rare (minor allele frequency, MAF, less than 0.05) and predicted to be detrimental, either by altering amino acids or splicing patterns, were prioritized.
Results
We identified numerous potentially damaging, ASD associated risk variants in genes previously unrelated to autism. A subset of these genes has been implicated in other neurobehavioral disorders including depression (SLIT3), epilepsy (CLCN2, PRICKLE1), intellectual disability (AP4M1), schizophrenia (WDR60), and Tourette syndrome (OFCC1). Additional alterations were found in previously reported autism candidate genes, including three genes with alterations in multiple families (CEP290, CSMD1, FAT1, and STXBP5). Compiling a list of ASD candidate genes from the literature, we determined that variants occurred in ASD candidate genes 1.65 times more frequently than in random genes captured by exome sequencing (P = 8.55 × 10-5).
Conclusions
By studying these unique pedigrees, we have identified novel DNA variations related to ASD, demonstrated that exome sequencing in extended families is a powerful tool for ASD candidate gene discovery, and provided further evidence of an underlying genetic component to a wide range of neurodevelopmental and neuropsychiatric diseases.
doi:10.1186/2040-2392-5-1
PMCID: PMC3896704  PMID: 24410847
Autism spectrum disorder (ASD); Identical by descent (IBD); Single nucleotide variant (SNV); Whole exome sequencing
22.  Evaluating mitochondrial DNA variation in autism spectrum disorders 
Annals of human genetics  2012;77(1):9-21.
SUMMARY
Despite the increasing speculation that oxidative stress and abnormal energy metabolism may play a role in Autism Spectrum Disorders (ASD), and the observation that patients with mitochondrial defects have symptoms consistent with ASD, there are no comprehensive published studies examining the role of mitochondrial variation in autism. Therefore, we have sought to comprehensively examine the role of mitochondrial DNA (mtDNA) variation with regard to ASD risk, employing a multi-phase approach.
In phase 1 of our experiment, we examined 132 mtDNA single-nucleotide polymorphisms (SNPs) genotyped as part of our genome-wide association studies of ASD. In phase 2 we genotyped the major European mitochondrial haplogroup-defining variants within an expanded set of autism probands and controls. Finally in phase 3, we resequenced the entire mtDNA in a subset of our Caucasian samples (~400 proband-father pairs). In each phase we tested whether mitochondrial variation showed evidence of association to ASD. Despite a thorough interrogation of mtDNA variation, we found no evidence to suggest a major role for mtDNA variation in ASD susceptibility. Accordingly, while there may be attractive biological hints suggesting the role of mitochondria in ASD our data indicate that mtDNA variation is not a major contributing factor to the development of ASD.
doi:10.1111/j.1469-1809.2012.00736.x
PMCID: PMC3535511  PMID: 23130936
mitochondrial DNA; autism; autism spectrum disorders; association studies; genetic
23.  Mycobacterial and mouse HSP70 have immuno-modulatory effects on dendritic cells 
Cell Stress & Chaperones  2012;18(4):439-446.
Previously, it has been shown that heat shock protein 70 (HSP70) can prevent inflammatory damage in experimental autoimmune disease models. Various possible underlying working mechanisms have been proposed. One possibility is that HSP70 induces a tolerogenic phenotype in dendritic cells (DCs) as a result of the direct interaction of the antigen with the DC. Tolerogenic DCs can induce antigen-specific regulatory T cells and dampen pathogenic T cell responses. We show that treatment of murine DCs with either mycobacterial (Mt) or mouse HSP70 and pulsed with the disease-inducing antigen induced suppression of proteoglycan-induced arthritis (PGIA), although mouse HSP70-treated DCs could ameliorate PGIA to a greater extent. In addition, while murine DCs treated with Mt- or mouse HSP70 had no significantly altered phenotype as compared to untreated DCs, HSP70-treated DCs pulsed with pOVA (ovalbumin peptide 323–339) induced a significantly increased production of IL-10 in pOVA-specific T cells. IL-10-producing T cells were earlier shown to be involved in Mt HSP70-induced suppression of PGIA. In conclusion, this study indicates that Mt- and mouse HSP70-treated BMDC can suppress PGIA via an IL-10-producing T cell-dependent manner.
doi:10.1007/s12192-012-0397-4
PMCID: PMC3682017  PMID: 23269491
Dendritic cell; HSP70; Arthritis; Mouse/murine; Tolerance
24.  EGF receptor trafficking: consequences for signaling and cancer 
Trends in Cell Biology  2014;24(1):26-34.
Highlights
•EGF receptor endocytic traffic can regulate signaling and cell survival.•Signaling from activated EGFR occurs at the endosome as well as the cell surface.•Endocytosis can have positive and negative effects on signaling and tumorigenesis.•EGFR traffic promoted by antineoplastic therapy is important in tumor resistance.
The ligand-stimulated epidermal growth factor receptor (EGFR) has been extensively studied in the analysis of molecular mechanisms regulating endocytic traffic and the role of that traffic in signal transduction. Although such studies have largely focused on mitogenic signaling and dysregulated traffic in tumorigenesis, there is growing interest in the potential role of EGFR traffic in cell survival and the consequent response to cancer therapy. Here we review recent advances in our understanding of molecular mechanisms regulating ligand-stimulated EGFR activation, internalization, and post-endocytic sorting. The role of EGFR overexpression/mutation and new modulators of EGFR traffic in cancer and the response to cancer therapeutics are also discussed. Finally, we speculate on the relationship between EGFR traffic and cell survival.
doi:10.1016/j.tcb.2013.11.002
PMCID: PMC3884125  PMID: 24295852
epidermal growth factor receptor (EGFR); endocytosis; trafficking; ubiquitination; oncogenes; antineoplastic therapy
25.  Assessing dynamics, spatial scale, and uncertainty in task-related brain network analyses 
The brain is a complex network of interconnected elements, whose interactions evolve dynamically in time to cooperatively perform specific functions. A common technique to probe these interactions involves multi-sensor recordings of brain activity during a repeated task. Many techniques exist to characterize the resulting task-related activity, including establishing functional networks, which represent the statistical associations between brain areas. Although functional network inference is commonly employed to analyze neural time series data, techniques to assess the uncertainty—both in the functional network edges and the corresponding aggregate measures of network topology—are lacking. To address this, we describe a statistically principled approach for computing uncertainty in functional networks and aggregate network measures in task-related data. The approach is based on a resampling procedure that utilizes the trial structure common in experimental recordings. We show in simulations that this approach successfully identifies functional networks and associated measures of confidence emergent during a task in a variety of scenarios, including dynamically evolving networks. In addition, we describe a principled technique for establishing functional networks based on predetermined regions of interest using canonical correlation. Doing so provides additional robustness to the functional network inference. Finally, we illustrate the use of these methods on example invasive brain voltage recordings collected during an overt speech task. The general strategy described here—appropriate for static and dynamic network inference and different statistical measures of coupling—permits the evaluation of confidence in network measures in a variety of settings common to neuroscience.
doi:10.3389/fncom.2014.00031
PMCID: PMC3958753  PMID: 24678295
functional connectivity; canonical correlation; coherence; ECoG; EEG; MEG

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